Environmental Management (2019) 64:272–286

https://doi.org/10.1007/s00267-019-01197-0

Impacts of Channel Morphodynamics on Fish Habitat Utilization

1
Parna Parsapour-Moghaddam ●
Colin P. Brennan1 Colin D. Rennie1 Chris K. Elvidge2 Steven J. Cooke2
● ● ●

Received: 6 December 2018 / Accepted: 22 July 2019 / Published online: 1 August 2019
© Springer Science+Business Media, LLC, part of Springer Nature 2019

Abstract
It is reasonable to expect that hydro-morphodynamic processes in fluvial systems can affect fish habitat availability, but the
impacts of morphological changes in fluvial systems on fish habitat are not well studied. Herein we investigate the impact of
morphological development of a cohesive meandering stream on the quality of fish habitat available for juvenile yellow
perch (Perca flavescens) and white sucker (Catostomus commersonii). A three-dimensional (3D) morphodynamic model
was first developed to simulate the hydro-morphodynamics of the study creek. The results of the morphodynamic model
were then incorporated into a fish habitat availability assessment. The 3D hydro-morphodynamic model was successfully
calibrated using an intensive acoustic Doppler current profiler (ADCP) spatial survey of the entire 3D velocity field and total
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station surveys of topographic changes in a meander bend in the study creek. Two fish sampling surveys were carried out at
the beginning and the end of the study period to determine presence–absence of fish as an indicator of the habitat utilization
of each fish species in the study reach. It was shown that morphological development of the stream was a significant factor
for the observed changes in the habitat utilization of juvenile yellow perch. It is shown that juvenile yellow perch mostly
utilized habitat where deposition occurred whereas they avoided areas of erosion. The results of this study and the proposed
methodology could provide some insights into the potential impact of sediment transport processes on the fish occurrence,
and distribution and has implications for management of small fluvial systems.
Keywords 3D morphodynamic modeling Morphological changes Fish habitat modeling Fish habitat utilization Yellow
● ● ● ●

perch White sucker

●

Introduction system morphodynamics. Appropriate choice of the mor-

Morphodynamic Modelling
Studies of the morphological behavior of fluvial systems are
crucial for understanding the associated quality and avail-
ability of aquatic habitat. However, morphodynamic pro-
cesses have been recognized as some of the least understood
phenomena in natural fluvial systems (Wu 2007). Several
morphodynamic models have been developed over the past
decades in attempt to improve the understanding of fluvial
* Parna Parsapour-Moghaddam
p.parsapour@uottawa.ca
1 models are more capable of reproducing complex 3D stream
Department of Civil Engineering, University of Ottawa, 161 Louis
Pasteur, Ottawa, ON K1N 6N5, Canada
2 models, and due to the advancement of computer technol-
Fish Ecology and Conservation Laboratory, Department of
Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON
K1S 5B6, Canada
phodynamic model depends on the condition and com-
plexity of the study area (Papanicolaou et al. 2008). Until
recently, the state-of-the-art for morphodynamic modeling
involved one-dimensional (1D) or two-dimensional (2D)
models (Pinto et al. 2012). However, direction and magni-
tude of bed shear stress, which has a significant influence on
sediment transport, may not be accurately estimated from a
1D or a 2D model (Lesser et al. 2001). This could be the
case in particular for meandering streams with dominant
secondary flow structures, wherein secondary flow occur-
rence can increase the sidewall shear stress exerted on
stream banks (Papanicolaou et al. 2007). Furthermore, due
to the complex nature of cohesive sediments, prediction of
the erosion and sedimentation patterns of a cohesive bed
stream is even more challenging. Three-dimensional (3D)
hydro-morphodynamics processes compared to 1D and 2D
ogy, development of 3D hydro-morphodynamic models has
Environmental Management (2019) 64:272–286
become more common recently (e.g., Rüther and Olsen
2005; Khosronejad et al. 2007, 2015).
One of the widely used hydro-morphodynamic open
source codes is Delft3D, which is developed by Deltares and
has a broad range of applications in fluvial systems studies
(e.g. Spruyt et al. 2011; Williams et al. 2013, 2016; Kasvi
et al. 2015a, b). The morphological module of Delft3D has
been validated by Lesser et al. (2004). This code can be
further divided to hydrostatic and non-hydrostatic 3D
modules. Parsapour‐Moghaddam and Rennie (2017) showed
that the hydrostatic module is able to predict the secondary
flow in a sharply meandering creek. Despite the growing
need for 3D morphodynamic modeling, only a few studies
have employed Delft3D for 3D morphodynamic modeling in
meandering streams. Students in Kleinhans’s lab (Kleinhans
et al. 2008; Schuurman et al. 2013; Schuurman and Klein-
hans 2015) have employed Delft3D to create 3D models to
predict morphodynamics of meandering and braided rivers.
Their studies have mostly focused on bifurcation dynamics
with non-cohesive sediments. Kasvi et al. (2015a) studied
the sensitivity and functionality of 2D and 3D hydro-
morphodynamic Delft3D models. Their results focused on a
sandy bed river bend and were limited to short-term (one
flood event) morphodynamic processes.
Fluvial System Morphodynamics and Fish Habitat
Dynamic interaction of the hydro-morphodynamic pro-
cesses and the aquatic environment define a fluvial system’s
ecological characteristics (Poff and Zimmerman 2010). In
order to improve the conditions of an aquatic ecosystem, it
is essential to know how fish populations respond to eco-
logical changes and how different fish species are linked to
their habitats (Portt et al. 2006). Fluvial system hydro-
morphodynamics influence the quality of habitat for fish
and other aquatic species (Baranya et al. 2018; Tamminga
and Eaton 2018). Suspended sediment transport can influ-
ence the water temperature and dissolved oxygen levels,
and can lead to biological impacts on aquatic organisms
(Kjelland et al. 2015). It is important to study the mor-
phological changes in fluvial systems and the corresponding
sediment loads to manage and preserve fish populations
(Sullivan and Watzin 2010).
Numerical simulation of fish habitat has been employed
since the 1980s as a useful means for fluvial system man-
agement and environmental impact assessment (Mouton
et al. 2007). Fish habitat models can quantify a fluvial
system’s ecological condition. They can also be used to
investigate the impact of different restoration plans and
fluvial system management measurements (De Kerckhove
et al. 2008). Several fish habitat models have been devel-
oped to predict the impact of ecological changes in fluvial
systems on fish abundance and diversity. Such models can
273
be employed to preserve an aquatic habitat or declining
species (Tash and Litvaitis 2007).
There have been few previous attempts to couple mor-
phodynamic model predictions with fish habitat modeling.
Kerle et al. (2002) and Baptist et al. (2002) indicated that
long-term morphodynamic changes in man-made secondary
channels in the Rhine River could significantly affect the
quality and availability of fish habitat. Baptist et al. (2002)
used a 2D version of Delft3D to model the hydro-
morphodynamics and the outputs were then fed into a
fuzzy habitat model, CASiMiR. However, no fish sampling
survey was conducted during their study so the fish habitat
model could not be validated. Accordingly, the relationship
between the morphodynamic changes and the availability of
the fish habitat was not studied. Hauer et al. (2007) showed
that riffle instability would negatively affect the reproduc-
tion of nase (Chondrostoma nasus), the main fish species in
the Austrian lowland Sulm River. They suggested that
morphological studies should be considered in river
restoration projects. Hauer et al. (2008) subsequently stu-
died how juvenile nase could be impacted by morphody-
namic processes in the river. They combined the results of
1D and 2D hydrodynamic models with a fish habitat model.
They obtained the sedimentation and erosion of the study
river by terrestrial surveys within 3 years. They then con-
ducted an electrofishing survey to study how the juvenile
nase respond to the morphological changes. The results of
this study confirmed the reduction in habitat suitability due
to channel morphological changes; however, no morpho-
dynamic simulation was employed. Moreover, the correla-
tion of the sedimentation and erosion with the available fish
habitat was not studied. Escobar‐Arias and Pasternack
(2010) assessed the functional flow based on the shear stress
dynamics to improve ecological functionality of a stream.
The ecological functions they considered included spawn-
ing, embryo incubation, emergence, and the river bed
changing period. This study did not include the linkage
between the intricate sediment transport processes and the
fish habitat. Noack (2012) used the CASiMiR habitat model
to simulate the suitability of a river bed for reproduction of
gravel-spawning fish. This study used a 3D morphodynamic
model to account for the morphodynamic processes and
considered the impact of bed level changes on the hydrau-
lics. However, the habitat model used in this study was
mainly based on the water depth, flow velocity, and
dominant substrate; the dynamic sedimentation and erosion
processes were not included in this model. Despite all the
effort to characterize the physical habitat and its require-
ments, additional research is still required to understand
relations between the aquatic ecosystem and physical
habitat (Hardy 1998; Escobar‐Arias and Pasternack 2010).
In particular, based on this review of the literature there
appear to have been no previous direct examinations of
274
relations between sedimentation/erosion processes and fish
occurrence, which is an important research gap to be filled.
Objectives
Ecological condition of a fluvial system, to a great extent,
depends on its physical habitat (Maddock 1999). Previous
morphodynamic-fish habitat studies have mostly focused on
the sediment grain size and distribution rather than the
pattern and location of erosion and sedimentation. The long-
term impacts of sediment transport on aquatic species are
still not well understood and more study is needed to alle-
viate the negative effects of sediment transport on fish
communities (Kjelland et al. 2015). It is of practical and
essential importance to identify and protect fish that are
sensitive to channel sedimentation and the associated sedi-
ment loads (Sullivan and Watzin 2010).
The present study, to the best of our knowledge, for the
first time, studies the relations between morphological
development and the fish occurrence in the same fluvial
system. In this study, we focused on the fish
presence–absence to examine the habitat utilization. We
developed a 3D Delft3D model of a natural cohesive
meandering stream using unsteady flow with the aim that
this methodology and parameters employed therein could
be useful in similar case studies. Total station topographic
surveys were conducted in 2014 and 2016 to provide
bathymetric change data for the morphodynamic module
calibration. We also conducted spatially intensive acoustic
Doppler current profiler (ADCP) surveys in the study area
to obtain data for the hydrodynamic module calibration. The
calibrated 3D morphodynamic model was then run for a
one-year period to attain the morphological development of
the study fluvial system. The data were employed to assess
how the fish presence changed over this period. We
Ottawa
Fig. 1 a Location of the City of Ottawa in Canada (adapted from
https://www12.statcan.gc.ca). b Study creek shown with the square
(adopted from Google earth), flow from west (left) to east (right). The
Environmental Management (2019) 64:272–286
performed two fish sampling surveys in the study area in
2014 and 2015 to find a relationship between the erosion-
sedimentation process and the fish habitat utilization. The
results of the 3D morphodynamic model were then incor-
porated in the fish habitat development. The main objectives
of this study can be summarized as:
a. Develop a 3D morphodynamic model of a cohesive
meandering channel;
b. Conduct a comprehensive field-measurement cam-
paign including total station, ADCP and fish sampling
surveys;
c. Compare the morphodynamic model results to actual
measured bed elevation changes;
d. Evaluate relations between selected fish species
occurrence and modeled morphological channel
characteristics;
e. Develop a fish habitat model incorporating the
channel morphological development.
Study Area
The study site was a meandering reach of Watts Creek,
which flows into the Ottawa River at Shirley’s Bay in the
Kanata region of the Municipality of Ottawa, Canada. Watts
Creek flows east and north over National Capital Com-
mission (NCC) greenbelt forest property (Fig. 1). The
catchment drainage area to the study reach is ~20 km2 and is
characterized by urban development in the headwaters
(68%) with the middle catchment area surrounding the
reach of interest composed of active agricultural (20%) with
some island forests and a forest/meadow buffer around the
creek (12%). Catchment elevations range from ~115 masl in
center point of the reach is situated at ~431,086.6 m E 5,021,107.4 m
N. Note the City of Ottawa rail line immediately adjacent to the south
of the creek
Environmental Management (2019) 64:272–286
the Watt’s Creek headwater to 68 masl at the study site to
56 masl downstream of the study reach at the confluence
with the Ottawa River. The channel slope is moderate along
the Watt’s Creek upstream branch, decreasing from 1% for
the first 3400 m to 0.5% for the next 2200 m, and is low
through the main channel and through the study reach
(~0.02%). Core samples of bed sediment collected from the
reach were identified as cohesive soils (Salem and Rennie
2017). Watts Creek provides crucial cool water fish habitat
and has a high fish abundance (Maarschalk-Bliss 2014). The
channel bed is characterised by periodic patches of dense
vegetation and alternating open areas, the overbanks are
typically well vegetated by grasses, trees, and shrubs pro-
viding a range of shade cover from full sun to full shade.
However, this creek has undergone erosion and degradation
(driven by rapid flow response to urban runoff and an increase
in wet–dry cycles for bank material), which can negatively
impact the available aquatic habitat. The present study
attempts to understand the hydro-morphodynamics to gain a
better understanding of fish habitat quality in Watts Creek.
The study reach is adjacent to a rail line. The meander
confinement by the rail line has caused excessive erosion
and irregular meandering pattern in the reach (Parsapour-
Moghaddam and Rennie 2018b). Field reconnaissance of
the creek revealed instabilities in the inner banks of mean-
ders, as well as the downstream limb of the outer bends. It
was also observed that a concave-bank bench has been
generated on the upstream portion of the outer bank at the
last sharp bend (Parsapour-Moghaddam and Rennie 2018b).
These observations confirmed that the study reach is an
active and unstable channel.
Methodology
The methodology employed in this study includes three
main components: (1) field studies, which involved terres-
trial surveying, ADCP measurements of stream depths and
a b
Fig. 2 Total station bathymetric points collected during summer: (a) 2014 (b) 2016. Flow from left to right. Background pictures taken from
Google Earth
275
velocities, and fish sampling; (2) 3D morphodynamic
modeling in which, using the field measurements, we
developed a 3D morphodynamic model to simulate the
hydro-morphodynamic processes of the study creek; and,
(3) fish habitat studies in which we evaluated the impact of
channel morphodynamics on the fish habitat utilization. The
results of the presence/absence data obtained from the fish
sampling surveys were linked to the results of the developed
morphodynamic numerical model. We also developed a fish
habitat model to examine how incorporating the river
morphodynamics can impact the predicted results of a fish
habitat model. Each of the three mentioned methodological
components are discussed in the following sections.
Field Studies
Initial bathymetric data needed for the morphodynamic
modeling was first collected during summer 2014 using a
total station survey with an average spacing of 1.2 and
0.3 m in streamwise and transverse directions, respectively
(Fig. 2a). We also conducted a Total station bathymetric
survey in the second meander bend of the creek during
summer 2016 to assess the morphological changes of the
stream within the 2-year period (Fig. 2b). Bathymetric
points were collected with an average spacing of 2.7 and
0.6 m in streamwise and transverse directions, respectively.
Triangular interpolation method (TIN) was then employed
in ArcGIS10.2 to attain the digital elevation model (DEM)
for both bathymetric surveyed data points.
We also employed a spatially intensive ADCP method to
obtain the spatial distribution of 3D velocities all over the
reach. An ADCP is a hydroacoustic tool which, based on
the principles of Doppler shift, measures the 3D flow
velocities. More detailed information on ADCP theory is
available in Simpson (2001), Simpson and Oltmann (1993),
and Rennie and Church (2010). We mounted a Sontek M9
River Surveyor ADCP on an Ocean Sciences trimaran riv-
erboat, which was operated and moved in a zigzag pattern
276
Fig. 3 Field studies in Watts
Creek. a ADCP mounted on an
Ocean Sciences trimaran
riverboat employed for spatially
intensive ADCP survey. b Total
Station used for the
terrestrial survey
via ropes by two operators at each side of the stream. The
sampling frequency of the moving boat was 1 Hz. The
compass was calibrated in situ through ADCP rotation with
varying pitch and roll. The spatial distribution of 3D velo-
cities, obtained from the ADCP survey, was then employed
to calibrate the 3D hydrodynamic model. Calibration of the
3D hydrodynamic model with this method ensures better
prediction of the 3D flow field (Parsapour-Moghaddam and
Rennie 2018a). Figure 3 shows field studies equipment
employed in the present study.
3D Morphodynamic Modeling
For 3D hydro-morphodynamic modeling of the study
meandering creek, we employed the Delft3D modeling
package (Delft-Flow version 4.01.01). Delft3D is a freely-
available, open-source code developed by Deltares. This
code includes different components interacting individually
or in combination with other modules over a mutual inter-
face (Deltares 2014). It is capable of modeling 2D or 3D
hydro-morphodynamics over a rectilinear or a
curvilinear grid.
The horizontal grid was generated using orthogonal
curvilinear grid cells covering the model domain (Fig. 1b).
The initial bathymetry was obtained using the interpolated
surveyed bathymetric data from the 2014 Total station
survey. To test the sensitivity of the model to the mesh,
several grids were developed and examined. A proper grid
cell resolution (average grid size of 80 cm) was attained
considering the balance between the computational cost and
grid cell resolution with a 6 s time step to meet the stability
condition. Grid cell properties were examined to ensure the
quality of the generated grid, i.e., aspect ratio <2 and
orthogonality <0.05 (Fig. 4).
Time series of discharge and water level were used for
the upstream and downstream boundary conditions,
respectively. SWMHYMO hydrologic modeling software
Environmental Management (2019) 64:272–286
was employed to simulate the continuous upstream
boundary discharge and downstream water level (Brennan
et al. 2018).
The hydrodynamic module was calibrated using the
procedure described by Parsapour-Moghaddam and Rennie
(2018a). Manning roughness and horizontal eddy viscosity
were the calibration parameters, and the hydrodynamic
module output was calibrated using spatially intensive
surveyed ADCP data. That is, 3D simulated velocities were
compared with the 3D measured ADCP throughout the
entire reach obtained on October 2015 (~0.5 m3/s).
Morphodynamic model calibration was achieved using
the data from the two topographic surveys in one channel
bend (Fig. 2). For calibration purpose, it was assumed that
the input hydrograph in the second year (2015–2016) was
the same as the first year (2014–2015) with a similar cycle.
Several morphodynamic parameters, such as the erosion
parameter, settling velocity, initial sediment layer thickness,
critical bed shear stress for erosion and deposition, and
horizontal eddy diffusivity were tested to find the sensitivity
of the model to each. The model was most sensitive to the
horizontal eddy diffusivity and the critical shear stresses for
erosion and deposition, thus these parameters were used for
morphodynamic model calibration.
Fish Habitat Studies
In order to link the fish habitat quality with the erosion and
sedimentation rate, fish sampling surveys were conducted in
the creek using backpack electrofishing. Electrofishing is
among the widely used methods for fish sampling surveys
(e.g. Sharber and Sharber Black 1999; Rosenberger and
Dunham 2005; Temple and Pearsons 2007). To be able to
assess how the fish occurrence was changed by the mor-
phological changes of the stream, two different fish sam-
pling surveys were conducted during summer 2014 and
summer 2015, which were, respectively, at the beginning
Environmental Management (2019) 64:272–286
Fig. 4 Generated mesh
properties: (a) aspect ratio and
(b) grid orthogonality
and end of the study period. Based on ADCP measurements
collected immediately following sampling in both 2014 and
2015, the flow discharge was, respectively, ~0.06 and
~0.08 m3/s and the temperature was ~18 °C during both
surveys. The results of the ADCP field measurements
confirmed that the fish sampling surveys were conducted
during similar low-flow conditions. Equivalent sampling
procedure and effort were employed during both sampling
events. The creek was divided into 5 m long subreaches
(21 subreaches) covering all the study reach except for the
very upstream end of the reach.
Fish sampling was started from downstream of the reach
toward the upstream. All fish caught within discrete sub-
reaches were measured to the nearest mm and identified
separately. All species were collected to ascertain the spe-
cies with the most abundant number of juvenile individuals
for further analyses. The two species found to be most
abundant during sampling were yellow perch (Perca fla-
vescens) [N = 121, total length 80.38 mm ± 7.34 mm, mean
± SD] and white sucker (Catostomus commersonii) [N = 39,
77.97 mm ± 35.49 mm]. Yellow perch are a cool-water fish
common throughout Eastern North America, and are
usually found in shoals near vegetation and other sub-
merged structures in lakes and pools in slow-moving
streams (Suthers and Gee 1986; Paukert et al. 2002; Froese
and Pauly 2018). They are more common in clear water and
abundance generally decrease with increasing turbidity
(Krieger et al. 1983). White sucker are an indiscriminate
bottom-feeding species with broad environmental
277
tolerances (Froese and Pauly 2018) that is relatively abun-
dant in the Midwest and Northeast regions of North
America (Saint-Jacques et al. 2000), and are found near all
types of substrates in lakes, streams, and rivers (Minnesota
DNR 2018).
To study the linkage between the fish habitat utilization
and the stream morphodynamics, we employed the results
of the developed 3D hydro-morphodynamic model. The
simulated results of cumulative erosion and sedimentation
within a one-year monitoring plan (August 2014–August
2015) were spatially analyzed to calculate their statistics in
each 5-m subreach. These results were compared to
observed changes in the presence–absence of both yellow
perch and white sucker during the study period. Specifi-
cally, analysis of variance (ANOVA) tests and multiple
comparison Tukey test (Tukey 1953; Kramer 1956) were
used to test if the predicted morphological changes had a
significant influence on habitat utilization of the fish. We
also analyzed the significance of other variables, such as
mean predicted values of sediment concentration, flow
depth, and depth-averaged velocity, on the habitat utiliza-
tion of yellow perch and white sucker in 2015. The results
of the fish sampling surveys were statistically analyzed
against different category of the hydro-morphodynamic
variables to study which group of the variables could have a
significant impact on the habitat utilization.
The results of the developed 3D hydro-morphodynamic
model were then incorporated in development of a habitat
model for fish species whose presence–absence was
278
impacted by the river’s morphology. For fish habitat mod-
eling, we used habitat suitability index (HSI) modeling,
which is the most common way to study the fish response to
their habitat (Noack 2012). An HSI provides a measure of
the quality of a given habitat variable to support particular
fish at different life stages, with values ranging from 0 (the
most unsuitable condition) to 1 (optimal condition) (Bovee
1986). In other words, the HSI indicates degree of habitat p
by fish and is shown by a univariate function (habitat suit-
ability curve) (Boavida et al. 2013). The standard hydraulic
habitat variables employed in the literature are commonly
flow depth, velocity, and substrate (Leclerc et al. 1995).
In the present study, results of the developed 3D mor-
phodynamic model were employed as inputs for these fish
habitat models. That means for the simulated result of each
grid cell of the numerical model, we assigned an HSI value
of 0–1 for each hydro-morphodynamic variable in accor-
dance with the available habitat suitability curves. We
employed two different scenarios based on the: (I) hydraulic
variables such as flow depth, velocity, and substrate. (II)
Hydraulic variables in addition to the morphological chan-
ges (i.e. erosion/sedimentation). For both scenarios, to
combine the results of HSI modeling based on different
hydro-morphodynamic variables, we used the arithmetic
mean to obtain a composite habitat suitability index (CSI):
Pn
HSIi
CSI ¼ i¼1 ð1Þ
n
Results
The hydrodynamic module of the developed 3D model was
first calibrated for the Manning roughness and horizontal
eddy viscosity using fully 3D ADCP velocities. The mor-
phodynamic module was then calibrated for horizontal eddy
diffusivity, critical bed shear stress for both erosion and
sedimentation to which the 3D model was more sensitive.
The calibrated parameter values are shown in Table 1.
Figure 5 shows the results of observed stream morphological
Fig. 5 Morphological changes
over the study period
(2014–2016) in one bend within
the study reach. a Results of the
3D morphodynamic model. b
Observed changes based on total
station surveys. Positive values
indicate deposition and negative
values indicate erosion. Flow
from left to right
Environmental Management (2019) 64:272–286
changes and the calibrated 3D morphodynamic model from
August 2014 to August 2016. As mentioned in Section 3.1,
the observed stream bend morphological development was
calculated by differencing two total station surveys. As is
shown, the calibrated model is in good agreement with the
terrestrial measurements. Some discrepancies could still be
seen close to the outer bank, which can be attributed to the
simple bank algorithm used in Delft3D. Deposition occurred
on the outer bank which is consistent with what was reported
by Parsapour-Moghaddam and Rennie (2018b). The results
of their field study showed the generation of reverse flow
eddies, which were interpreted to have caused the develop-
ment of the concave bank bench in the study reach.
Blanckaert et al. (2013) reported an occurrence of a dead
water zone in the outer-bank widening of an open channel
bend with an immobile gravel bed. It was shown that
channel widening could promote a weak horizontal recir-
culation eddy. Similarly, the modeled outer bank deposition
in the study creek can be attributed to the widening meander
bend which reduces the flow velocities and consequently
causes an outer bank deposition. The calculated mean
absolute error of the bathymetric change is 0.11 m. It can be
seen that the erosion is underestimated and deposition is
overestimated, but the locations of erosion and deposition
are modeled reasonably accurately. Considering all the
uncertainties inherent to sediment transport modeling, these
results are promising. Accordingly, the developed 3D model
could be further employed to predict the hydro-
morphodynamics of the study creek.
Table 1 Calibration results of the developed 3D hydro-
morphodynamic model
Calibration parameters Values
Manning roughness 0.015
Background horizontal eddy viscosity 1 m2/s
Background horizontal eddy diffusivity 4 m2/s
Critical bed shear stress for erosion 0.35 N/m2
Critical bed shear stress for sedimentation 0.35 N/m2
Environmental Management (2019) 64:272–286
Fig. 6 3D morphodynamic
model results at the end of the 1-
year study period: (a) depth-
averaged velocity, (b)
suspended sediment transport,
(c) flow depth, and (d)
cumulative morphological
development of the study creek.
Flow from left to right
The calibrated 3D model was then run from August 2014
to August 2015. Figure 6 shows the results of the developed
3D model during the one-year study period. Figure 6d
shows morphological development of the study area. These
results were also qualitatively consistent with the actual
morphological changes based on the field reconnaissance in
terms of the pattern and location of the sedimentation and
erosion (Parsapour-Moghaddam and Rennie 2018b).
Figures 7 and 8 show presence–absence of white sucker
and yellow perch during the two fish sampling surveys,
respectively. Figure 9 illustrates the changes in the presence
of these two fish species with respect to the morphological
changes during the study period. Since both fish sampling
surveys were conducted at the same time of year under very
similar flow conditions and temperature, it may be reason-
able to attribute the fish presence changes to the stream
morphological changes.
As shown in Fig. 9, presence of yellow perch mainly was
gained in zone 3, where sediment deposition was mostly
predicted. On the other hand, no consistent trend could be
observed for white sucker in this zone, since presence was
gained in four sampling subreaches, lost in one subreach,
and had no change in the other five sampling subreaches. In
zone 2 where erosion was mostly dominant, the presence of
yellow perch was lost or had no change. However, white
sucker presence mostly increased in this zone. In zone 1,
which had a mix of erosion and deposition, presence by
yellow perch was increased in two subreaches while in the
other three subreaches no change was observed. The white
279
sucker presence did not change in this zone during the study
period. ANOVA tests were carried out to identify any sig-
nificant relations between the model morphodynamic results
and changes in the fish presence. Simulated changes in bed
elevation during the 1-year study period in each 5-m sam-
pling were compared to observed changes in habitat utili-
zation of fish within each sub-reach. ANOVA test results
yielded P values of 0.035 and 0.239 for yellow perch and
white sucker, respectively. The results of ANOVA test
confirmed that the morphological changes during the study
period were a significant factor for change in presence of
yellow perch at the 5% significant level, whereas white
sucker presence was not significantly affected by the ero-
sion and sedimentation.
We also evaluated the influence of different habitat
variables on fish presence–absence within the reach. This
was achieved using ANOVA multiple comparison tests
(Table 2) to study if the flow depth, depth-averaged velo-
city, and suspended sediment transport had any impact on
the presence–absence of yellow perch and white sucker at
the end of the 1-year study period. Each variable was
classified into three different categories (low, medium,
high) as shown in Table 2.
As is shown in Table 2, yellow perch utilization was
significantly affected by low suspended sediment transport
and low depth-averaged velocity within each sampling
subreach. However, white sucker showed significant influ-
ence of only medium depth-averaged velocity. Since the
ANOVA test suggested juvenile yellow perch
280
Fig. 7 Presence–absence of
white sucker in: (a) 2014 and
(b) 2015
Fig. 8 Presence–absence of
yellow perch in: (a) 2014 and
(b) 2015
presence–absence was significantly impacted by morpho-
logical changes, HSI models were subsequently developed
for juvenile yellow perch to simulate its potential habitat
preference in the study creek. In order to develop an HSI
fish habitat model, we used habitat suitability curves
available for yellow perch based on flow depth, velocity,
and substrate according to Krieger et al. (1983). The creek
bed substrate is mostly preferred particle size for the
Environmental Management (2019) 64:272–286
juvenile yellow perch, which according to Krieger et al.
(1983) is <0.062 mm. The outputs of the developed 3D
morphodynamic model were inputted into the fish habitat
model. After finding the HSI value of each hydro-
morphodynamic variable (i.e., flow depth, velocity, sub-
strate, and erosion/deposition), we calculated a composite
habitat suitability index based on the arithmetic mean of the
HSI values within each numerical grid cell. These results
Environmental Management (2019) 64:272–286 281

Fig. 9 Changes of presence

during the 1-year study period:
(a) yellow perch and (b) white
sucker. Morphological changes
of each zone (1, 2, 3) in the
study reach

Table 2 Statistical analysis

Hydro-morphodynamic variables Range
based on the multiple
comparison ANOVA test. Low Medium High
Significantly different variables
are highlighted. Range of each Fish species
variable category is specified in Yellow perch
the table
Depth averaged velocity (m/s) 0.1–0.15 0.15–0.2 0.2–0.28
Suspended sediment (m3/s/m) 0.04–0.06 0.06–0.08 0.08–0.1
Depth (m) 0.1–0.2 0.2–0.4 0.4–0.6
White sucker
Depth averaged velocity (m/s) 0.1–0.15 0.15–0.2 0.2–0.28
Suspended sediment (m3/s/m) 0.04–0.06 0.06–0.08 0.08–0.1
Depth (m) 0.1–0.2 0.2–0.4 0.4–0.6

Fig. 10 Predicted habitat

suitability map for juvenile
yellow perch based one: (a)
scenario I and (b) scenario II
(with consideration of the
morphological changes)

are shown in Fig. 10. It should be noted that to incorporate fish habitat studies confirmed that yellow perch were mostly
the morphological changes in calculation of the HSI model observed in zones where deposition occurred.
in scenario II (Fig. 10b), in the areas of erosion and The suitability of each fish habitat model can be assessed
deposition we applied HSI of 0 and 1, respectively, since by comparing Fig. 10 to the observed juvenile yellow perch
282
utilization of habitat (Fig. 8b). It can be concluded that
scenario II could better predict the habitat quality in zone 3
(refer to Fig. 9 for locations of each zone) where the fish
sampling survey showed the presence of fish. This higher
degree of habitat preference by fish is better predicted when
the morphological impacts was taken into account. In zone
2, both scenarios estimated less likelihood of the fish pre-
sence, which is consistent with the fish absence during the
fish sampling surveys (Fig. 8b). As for zone 1, scenario I
predicted very similar habitat preference all over the zone.
However, based on the fish sampling surveys, yellow perch
was present in two sampling subreaches and absent in the
other subreaches. This higher habitat preference of fish in
zone 1 was better predicted in scenario II. In general, it can
be concluded that the habitat preference and variability was
better predicted in scenario II in which the morphological
changes were taken into account. Consideration of the
morphological changes to the fish habitat model leads to a
habitat model specifically parameterized in accordance with
the fluvial system’s eco-morphological conditions.
Discussion
It can be reasonably expected that the hydro-
morphodynamic processes of a fluvial system can affect
the quality and availability of fish habitat given the strong
and inherent connections between streams and their biota
(Lapointe et al. 2014). Nevertheless, the impact of fluvial
system morphological changes on fish habitat is yet poorly
studied. The study herein considered channel morphody-
namics in fish habitat modeling. This could be of practical
importance river restoration strategies where fish habitat
quality for a certain time period is understood, but change in
the habitat quality over time is required. The morphological
changes of a cohesive meandering creek, obtained from a
3D morphodynamic model, were correlated to changes in
the habitat utilization of juvenile yellow perch and white
sucker within a 1-year period. The results of the calibrated
morphodynamic model reasonably agree observed mor-
phological change obtained by terrestrial surveying. The
ability of the model to simulate this process confirms that
the developed model could reasonably be employed to
predict the morphological changes in this creek.
We carried out two fish sampling surveys, both of which
occurred during the same season of summer low flow with
very similar low-flow conditions. Based on our last col-
lected data and the antecedent precipitation and temperature
from the weather station, we are not aware of any sub-
stantial difference in the previous flow condition in two
sampling years. Accordingly, it is reasonable to assume that
hydrodynamic and other habitat variables, such as tem-
perature and dissolved oxygen were not significant factors
Environmental Management (2019) 64:272–286
in the observed changes in fish utilization of habitat
between surveys. Based on the results of this study, it can
be concluded that yellow perch was more susceptible to the
suspended sediment compared to white sucker. It was
demonstrated that juvenile yellow perch utilization of
habitat was significantly impacted by the morphological
changes and the lower suspended sediment transport. In
particular, yellow perch habitat utilization increased in areas
of deposition, possibly suggesting that yellow perch were
seeking habitat with lower suspended sediment concentra-
tion. In general, yellow perch and white sucker have dis-
tinctive characteristics and habitat preferences. White
sucker range over a larger domain within a river, while
yellow perch tend to have more specific physical micro-
habitat requirements and occupy slower flow zones where
deposition is more likely. Furthermore, white sucker are
associated with the river-bed whereas yellow perch prefer
water column habitat. If yellow perch feed in the water
column, suspended sediment could hinder their feeding
success. Accordingly, this can be the reason that they were
more impacted by the suspended sediment compared to
white sucker. Kjelland et al. (2015) reported that yellow
perch death was increased with elevated sediment con-
centration. The results of the present study support this
argument that yellow perch could be sensitive to the
stream’s morphological behavior. On the other hand, the
present study illustrated that white sucker was not sig-
nificantly impacted by the morphological changes and
suspended sediment concentration. This is consistent with
previous studies which reported that white sucker is tolerant
to varying environmental circumstances (Saint-Jacques
et al. 2000) and does not show health impairments when
exposed to increased levels of fine sand (Merten et al.
2010). It should be noted that this study mainly focused on
juvenile yellow perch and white sucker, while the results
may be different for other life stages of these fish species.
As the results showed significance of the sediment
transport on the yellow perch habitat selection, we devel-
oped an HSI habitat model to demonstrate the degree of
habitat preference represented by this fish species. It was
shown that the HSI model that included the channel mor-
phological changes could better predict the yellow perch
habitat preference. Previous studies showed that fish habitat
quality depends on the river type (Jungwirth et al. 2000).
Accordingly, site-specific HSI is often recommended
(Boavida et al. 2014). Consideration of the morphological
changes to the fish habitat model can provide a habitat
model specifically parameterized in accordance with the
study site’s eco-morphological conditions.
Similar to other fish habitat studies, there still may be
some uncertainties in these results related to the field
measurements and the numerical model predictions (Gard
2009). Previous studies have shown that 2D numerical
Environmental Management (2019) 64:272–286
models can be reasonably employed for fish habitat studies
(e.g., Boavida et al. 2014, Zingraff-Hamed et al. 2018).
However, application of a 2D model for a fish habitat study
is inevitably accompanied with errors in estimation of flow
velocity and depth (Boavida et al. 2013). To minimize these
errors, in the present paper, we employed a 3D numerical
model to better simulate the 3D flow field and the impact of
secondary flow on the river hydromorphodynamics. Suc-
cessful calibration and validation efforts by comparison
with the field measurements and the field reconnaissance
confirmed that the model was able to produce adequately
accurate representation of the key habitat variables. More-
over, using the averaged data set in each subreach for the
fish habitat studies minimizes the uncertainties associated
with the numerical model outputs in each numerical grid
cell while still considering the full 3D flow field.
Mathematical combination of hydromorphodynamic
variables (i.e., flow depth, velocity, substrate, and sedi-
mentation) in the habitat modeling may be also associated
with some uncertainties, since there are different methods to
integrate the variables (Muñoz-Mas et al. 2012). In the
present study, we applied the arithmetic mean in which it is
assumed that poor habitat quality of one variable can be
compensated by the rich habitat condition of another vari-
able (Noack 2012). This can be a reasonable assumption
since the quality of fish habitat depends on the combination
of all variables rather than separate impact of each variable
(Lambert and Hanson 1989). Moreover, the results of a
sensitivity analysis on different integration methods con-
firmed that the arithmetic mean can provide sufficiently
reasonable results (Parsapour-Moghaddam et al. 2017).
On the other hand, the velocity measurements can be
associated with some errors (Gard 2009; Boavida et al.
2013). In this study, we minimized possible velocity mea-
surement errors by conducting a spatially intensive ADCP
survey all through the reach (average velocity errors <10%).
This helps for more accurate and realistic comparison of the
model results with the measurements both vertically and
spatially through the reach. This can subsequently increase
the model prediction capability. Nevertheless, still, there
may be some errors due to the ADCP measurements (Par-
sapour-moghaddam and Rennie 2018a).
Another source of uncertainty can be due to the fish
sampling measurements. We attempted to minimize these
errors by standardizing electrofishing effort and sweep
techniques in both sampling years. Moreover, due to the
narrow width of the channel, it is reasonable to assume that
no emigration and immigration occurred between different
sampling transects. Moreover, we focused on the occur-
rence of the selected species, i.e., presence–absence. That is,
we examined what would be the preferred habitat for the
target fish to occupy, despite the availability of all areas.
This reduces the sensitivity of the results to the number of
283
surveyed fish and inter-operator variability in sampling
efficiency. Nonetheless, successful calibration and valida-
tion results of the numerical model suggests that most of the
uncertainties that may exist in the present study arose from
the biological measurement. Validation of the developed
fish habitat-morphodynamic model with multi-year data
could help to alleviate these uncertainties. Regardless,
similar to any other fish habitat study, the present study
employed some simplified assumptions to simulate the
biological response of fish in the real world. Although we
attempted to minimize the errors associated with the results,
these uncertainties are inevitable and cannot be completely
eliminated (Gard 2009; Boavida et al. 2013).
Nonetheless, to the best of our knowledge this study
represents the first attempt to validate a stream
morphodynamic-habitat model using fish sampling results.
The results of this research suggest that much further study
of the influence of channel morphodynamics on fish habitat
is warranted. For example, habitat suitability curves could
be developed based on the impact of morphological changes
and suspended sediment concentrations on yellow perch.
Conclusion
Morphological development of a cohesive meandering
creek was studied to discover if morphodynamic processes
could impact fish habitat utilization for juvenile yellow
perch and white sucker. Two fish sampling surveys were
carried out at the beginning and end of the study period.
Successful validation efforts indicated that the developed
model could be reasonably employed to predict the hydro-
morphodynamics of the study creek. ANOVA tests showed
that morphological development was a significant factor in
the habitat utilized by juvenile yellow perch, while juvenile
white sucker utilization of habitat was not significantly
impacted by the morphological changes in this creek. It was
shown that habitat utilization of juvenile yellow perch
mostly increased in the areas where sediment deposition
occurred. Results of multiple comparison ANOVA tests
illustrated that low depth-averaged velocity and low sus-
pended sediment transport were significant factors in habitat
utilization of juvenile yellow perch. On the other hand,
habitat utilization of juvenile white sucker was significantly
impacted only by the medium range of depth-averaged
velocity. Since juvenile yellow perch was sensitive to the
morphological changes, an HSI habitat model was devel-
oped to predict the habitat preference of juvenile yellow
perch. Accordingly, the results of the developed hydro-
morphodynamic model were fed into the fish habitat model
of juvenile yellow perch. The results demonstrated that the
fish habitat model for juvenile yellow perch yielded better
predictions of fish habitat utilization when the effect of
284 Environmental Management (2019) 64:272–286

morphological changes was taken into account. The present directions, respectively, and u, v, and w denote velocity
study suggested that a stream’s morphological changes may components; g is the gravitational acceleration; ρt is the
have an influence on fish habitat utilization. This could be a time; υh and υv are, respectively, horizontal and vertical
step toward better understanding and prediction of fish kinematic eddy viscosity coefficients.
habitat quality with respect to stream morphological chan- After applying the approach of Reynold’s averaging,
ges, providing some insights into the impact of sediment turbulence closure models are employed to solve the
transport on fish communities. This may enhance the Reynolds-averaged Navier–Stokes (RANS) equations.
aquatic habitat and have practical importance in the river Delft3D-Flow code is numerically solved based on the
management. More study is needed to understand the effect finite difference method. We employed σ coordinate
of morphological changes on various fish species in a range system in which the vertical layers are bounded by the
of fluvial environments. Preferably, future studies will planes which follow the free surface and the bottom
include more comprehensive fish population assessments topography. The k–ε turbulence closure model, based on
that consider inter-annual and intra-annual variability in eddy viscosity theory of Kolmogorov and Prandtl (Del-
both target and control reaches. tares 2014), was used to calculate the 3D turbulence. The
morphodynamic module of Delft3D is capable of simu-
Acknowledgements The authors wish to thank the National Capital lating the sediment transport of suspended load and
Commission (NCC); particularly, Bina Chakraburtty, for funding this
bedload for non-cohesive sediments and suspended load
research.
for cohesive sediments. As mentioned in Section 2, the
study creek has cohesive bed and bank materials. For
Compliance with Ethical Standards
suspended sediments, Delft3D solves the 3D advection–
Conflict of Interest The authors declare that they have no conflict of diffusion equation:
interest.      
∂c ∂uc ∂vc ∂ðw  ws Þc ∂ ∂c ∂ ∂c ∂ ∂c
þ þ þ ¼ Dx þ Dy þ Dz
∂t ∂x ∂y ∂z ∂x ∂x ∂y ∂y ∂z ∂z
Publisher’s note: Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. ð6Þ
where c is mass concentration of the sediment (kg/m3), Dx,
Dy, and Dz are sediment eddy diffisivities (m2/s), and ws is
Appendix sediment settling velocity (m/s). Eddy diffisivities and local
flow velocities are calculated according to hydrodynamic
The Delft3D hydrodynamic model solves 3D Navier–Stokes model results. Delft3D calculates the sedimentation and
equations for incompressible flow under Boussinesq erosion of the cohesive sediment employing the
assumptions. The partial differential equations include the Partheniades–Krone formulations (Partheniades 1965):
following flow and momentum continuity equations:
E ¼ MSðτcw ; τcr;e Þ ð7Þ
∂η ∂ðhUÞ ∂ðhVÞ
þ þ ¼0 ð2Þ
∂t ∂x ∂y D ¼ ws cb Sðτcw ; τcr;d Þ ð8Þ
 
Δzb
!   cb ¼ c z ¼ ;t ð9Þ
∂u ∂u ∂u ∂u ∂η ∂2 u ∂2 u ∂ ∂u 2
þ u þ v þ w ¼ g þ ν h þ þ νv
∂t ∂x ∂y ∂z ∂x ∂x2 ∂y2 ∂z ∂z
ð3Þ where E is erosion flux, M is a user-defined erosion para-
!   meter, D is deposition flux, cb is the average sediment
∂v ∂v ∂v ∂v ∂η ∂2 v ∂2 v ∂ ∂v concentration in the near bottom computational layer,
þ u þ v þ w ¼ g þ ν h þ þ νv
∂t ∂x ∂y ∂z ∂y ∂x2 ∂y2 ∂z ∂z Sðτcw ; τcr;e Þ is an erosion step function:
ð4Þ ( 
  τcw
τcr;e  1 ; when τcw >τcr;e
S τcw ; τcr;e ¼ ð10Þ
In shallow water applications, the vertical momentum 0; when τcw  τcr;e
equation is reduced to the hydrostatic pressure assumption:  
S τcw ; τcr;d is a deposition step function:
∂p
¼ ρg ð5Þ ( 
∂z   1  ττcr;d
cw
; when τcw <τcr;d
S τcw ; τcr;d ¼ ð11Þ
where h is the water depth, η is the water surface elevation, 0; when τcw  τcr;d
U and V are the depth-averaged velocities in x and y
Environmental Management (2019) 64:272–286
τcw is maximum bed shear stress due to waves and cur-
rent calculated through the wave–current interaction, τcr,e is
the user-defined critical shear stress for erosion, and τcr,d is
the user-defined critical shear stress for deposition.
The Delft3D morphodynamic module also includes bed
level update as well as the bank erosion. Bank erosion is a
function of erosion flux in the adjacent dry cell. In the
developed model, 50% of the erosion in the wet cell was
redistributed to the neighboring dry cells. Wet cells were
defined to have at least 10 cm of water depth.
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